Contacts of the strand formed by residues 131 - 135 (chain K) in PDB entry 3Q3G
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 131 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129K PRO 3.9 1.9 + - - -
130K PRO* 1.3 72.0 - - - +
132K VAL* 1.3 60.1 + - - +
133K TYR* 3.4 35.1 + - - -
152K LEU 3.2 5.2 - - - +
153K VAL* 3.6 2.1 - - - -
154K LYS* 2.8 39.4 + - - +
601K EDO 4.2 6.3 - - - -
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Residues in contact with VAL 132 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130K PRO* 4.3 10.1 - - + +
131K SER* 1.3 73.8 - - - +
133K TYR* 1.3 62.1 + - - +
151K CYS* 3.7 29.6 - - - -
152K LEU 3.5 3.6 - - - +
153K VAL* 4.7 3.1 - - + -
206K CYS* 4.2 5.8 - - - +
208K VAL* 3.8 35.0 - - + -
217K VAL* 3.9 30.7 - - + -
219K LYS* 3.5 20.5 - - + +
601K EDO 3.0 31.3 + - - -
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Residues in contact with TYR 133 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H PRO* 6.1 0.4 - - + -
127J SER* 3.5 24.5 - - - +
129J GLU* 4.0 11.7 - - + -
130J GLN* 3.5 49.0 + - + +
133J SER* 4.0 18.6 + - - -
131K SER* 3.4 34.0 + - - -
132K VAL* 1.3 77.8 - - - +
134K PRO* 1.3 65.8 - - - +
135K LEU* 5.8 1.6 - - + -
151K CYS* 3.6 3.3 - - - -
152K LEU* 2.8 66.7 + - + +
154K LYS* 4.2 12.8 - - + -
219K LYS* 4.9 0.4 - - - -
601K EDO 4.4 6.7 - - - -
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Residues in contact with PRO 134 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125J PRO 5.3 0.9 - - - +
127J SER* 3.7 21.1 + - - -
129J GLU* 3.6 38.8 - - - +
603J EDO 4.6 5.8 - - - +
133K TYR* 1.3 84.8 - - + +
135K LEU* 1.3 66.1 + - - +
136K ALA* 3.9 4.2 + - + +
150K GLY 4.1 0.2 - - - +
151K CYS* 4.9 0.4 - - - -
219K LYS* 4.1 19.3 - - + -
220K LYS 4.4 5.4 - - - +
221K ILE* 3.7 29.6 - - + -
222K VAL 5.3 1.8 - - - +
224K ARG* 5.3 2.3 + - - -
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Residues in contact with LEU 135 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124J PHE* 3.8 23.9 - - + +
125J PRO 4.7 8.1 - - - +
127J SER* 6.0 1.8 - - - +
137J SER 5.4 2.7 - - - +
139J VAL* 3.8 36.1 - - + -
141J PHE* 3.9 18.2 - - + -
133K TYR* 5.6 1.3 - - + -
134K PRO* 1.3 77.3 - - - +
136K ALA* 1.3 59.0 + - - +
149K LEU* 3.5 10.7 - - - +
150K GLY* 2.8 49.6 + - - +
151K CYS 3.5 27.1 - - - +
152K LEU* 4.0 18.6 - - + +
189K SER* 4.8 1.8 - - - -
221K ILE* 3.8 3.6 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il